This data accompanies Hess et al. (2026, Science Advances). It consists of Last Millennium (750 CE to present) Mg/Ca and other trace elemental measurements from a thermocline-dwelling planktonic foraminifera (Pulleniatina obliquiloculata) from the Indonesian Seas. Sediment cores BJ8-03 31MC and BJ8-03 32GGC are from the Makassar Strait and BJ8-03 6MC and BJ8-03 7GGC from the Java Sea. Mg/Ca values from Site BJ8-03 31MC have been corrected for analytical offsets from BJ8-03 32GGC. Hess et al. (2026) used temperatures derived using the species-specific calibrations of Hollstein et al. (2017), though those derived using the multi-species equation from Anand et al. (2003) are also provided. Ages were generated using geoChronR (McKay et al., 2021).